Wong has also done extensive voiceover work and stage acting. The most well known of his voice acting roles is that of Captain Li Shang from the Disney animated film Mulan. He would later reprise this role twice, most notably for the video game Kingdom Hearts II. Beginning in 2016, Wong appeared in the TV series Gotham as Hugo Strange.

Wong gained wide attention as a result of his Broadway debut in M. Butterfly opposite John Lithgow. The play won multiple awards, including several for Wong, who at that time ceased using his full name in favor of his initials. He has since ceased the use of punctuation in his initials.

In 1990, Wong objected to Actor’s Equity that the plan to use British actor Jonathan Pryce in the role of The Engineer in Broadway run of Miss Saigon, which Pryce had originated during the show’s extended run in London, would take jobs away from actors of Asian descent. Although the union barred Pryce from acting the role in response to Wong’s complaint, vociferous opposition from Charlton Heston and a threat by the musical’s creator and producer, Cameron Mackintosh, to cancel the American production entirely, induced the union to reverse course. Pryce went on to win a Tony award for Best Actor in a Musical for that role.

In 2008, he starred in the one-man show Herringbone, in which he portrayed 12 roles, at McCarter Theatre at Princeton University. He brought the show to the La Jolla Playhouse in San Diego the following year. In 2012, Wong starred in Herringbone to benefit Dixon Place in New York for two performances. The production, recorded live for a 2014 CD release, was his first appearance in New York of the material, timed to coincide with the 30th anniversary of the original New York production.

In 2014, Wong starred in the U.S. premiere of James Fenton’s acclaimed adaptation of The Orphan of Zhao, a classic Chinese legend that has its roots in the fourth century BC, directed by Carey Perloff at American Conservatory Theater (A.C.T.). The Orphan of Zhao is an epic story of self-sacrifice and revenge. In the aftermath of a political coup, a country doctor is forced to sacrifice his own son in order to save the last heir of a noble and massacred clan. The Orphan of Zhao was a co-production with La Jolla Playhouse.

Wong announced his departure from the cast of Law & Order: SVU in July 2011, to join another NBC police drama, Awake, in which he portrayed Dr. Johnathan Lee, a confrontational therapist of an LAPD detective (portrayed by Jason Isaacs) who lived in two realities.[5] Wong guest starred in a thirteenth season episode of Law & Order: SVU titled "Father Dearest" (which aired May 2, 2012).[6]

In 2015, he was named Artist-in-Residence at La Jolla Playhouse. Wong guest starred on a NCIS: New Orleans Episode 1.13 titled "The Walking Dead" (which aired February 3, 2015), where he portrayed Navy Lieutenant Commander Dr. Gabriel Lin.

Wong also guest-starred as the enigmatic Whiterose (who is head of The Dark Army) in Season 1's episodes 8 and 10 on USA Network's Mr. Robot. He also plays the dual role of Zhang, the Chinese Minister of State Security. He returned in recurring roles for the show's second season, but has been promoted to the main cast for the third season, which debuted October 11, 2017.

Beginning August 13, 2017, BD began hosting the new HLN series Something's Killing Me With BD Wong. The documentary explores strange and unexplainable, real medical ailments and attacks that may be gradual or descend rapidly. But in either case, if a cause and cure aren't found immediately, these real-life patients will die.

Wong is openly gay. He began a long-term relationship with talent agent Richie Jackson in 1988.[8] In 2000, the couple had twin sons—Boaz Dov, who died 90 minutes after birth, and Jackson Foo Wong—through a surrogate mother, using Wong's sperm and an egg donated by Jackson's sister. In 2003, Wong wrote a memoir about his experiences with surrogacy titled Following Foo: the Electronic Adventures of the Chestnut Man. Wong and Jackson ended their relationship in 2004.[8] Wong amicably co-parents his son with his ex-partner Jackson and Jackson's partner, Jordan Roth.[9] On October 7, 2018, he married Richert John Frederickson Schnorr, his partner of eight years, in Brooklyn, New York.[10]